REBELSCIENCE articles

Archiveuv package manager
Genome Toolkit Series

Genome Toolkit. Part 4.2: Modernizing the Existing Python Project

In Part 4.2, we modernize Genome Toolkit and turn our original project into a proper installable Python package. We move from Pipenv to uv, organize the code under src/, move our existing k-mer algorithms into the new package, and update application.py to use them. Most importantly, we keep the scientific calculations unchanged and verify that Genome Toolkit still produces exactly the same results.

Genome Toolkit Series

Genome Toolkit. Part 4.1: Building a Scientific Python Package

In Part 4.1, we take a step back and look at where Genome Toolkit is going next. We introduce refactoring, explain why our small project is ready to grow into a proper scientific Python package, and show how this gives us a cleaner foundation for future biological tools and experiments. We also look at something pretty exciting: by building Genome Toolkit properly now, we are gradually making it AI-ready for future APIs, MCP tools, and AI agents.